Oh, I see it now in that pic Colyn posted. You may grind off too much material. I don't think you'll be able to get flush with it. It may be best to sell that notch, and have a custom one done.
Yes it is on both sides of the frame. I would personally feel safe with a AVS only because its so much bigger and you would cut most of it away then could grind what's left off and box the back side of the frame.
I would go with either AVS or custom built depending on which was cheaper. If you don't go any bigger than the avs then you won't have to cut the bed floor only part of the bed crossmember.